Asked in a situation where you reach a point of no return or you have surpassed a dangerous obstacle and have survived the ordeal. 'What now' is also used as in,'where does this leave us', in terms of re-questioning your relationship status with someone.

Butch: What now?
Marsellus: What now? Well, let me tell you what now. I'm gonna call a coupla pipe-hitting' niggas, who'll go to work on the homes here with a pair of pliers and a blowtorch. Hear me talkin', hillbilly boy?! I ain't through with you by a damn sight. I'm gonna get Medieval on your ass.
Butch: I meant what now, between me and you?
Marsellus: Oh, that 'what now?' Well, let me tell ya what now between me an' you. There is no me an' you. Not no more.

It is a question in most movie wherein the answer is "we wait". I'm sure you have heard or encountered this phrase being asked by the actor or some supporting actor to someone else especially in movies wherein the main characters are planning on something big... whether an escape, a rescue or whatever.